From: Axel Kohlmeyer (
Date: Tue May 06 2014 - 10:06:39 CDT

On Tue, May 6, 2014 at 10:58 AM, Passerone, Daniele <> wrote:

> thank you Axel.
> All what you write is clear, however let me insist like the "widow in the
> gospel" and try to propose a way.
> Pbwithin has access to the coordinate of the images of the neighbors of
> atom k.

​no it doesn't. it creates temporary buffer of positions around the
principal cell with the length of the "within-cutoff". this buffer is not
available outside of the command.

> Now, one could build a functions that adds new atoms at the coordinates
> used by pbwithin, and then addbond between the original atom k and these
> new atoms. What do you think? do you see any possibility there ?

no. ​this doesn't make sense either.​ it is not a good idea to speculate
about these things without a good understanding of how VMD works internally--001a11c1b680518bd004f8bc98d1--